Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate CA265_RS10520 CA265_RS10520 ABC transporter ATP-binding protein
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__Pedo557:CA265_RS10520 Length = 568 Score = 167 bits (424), Expect = 4e-46 Identities = 96/265 (36%), Positives = 163/265 (61%), Gaps = 12/265 (4%) Query: 3 LMELKGVSVIFEDKVGLFKKRKFY--ALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVG 60 L+++K + + GLF K Y A+ ++ + G+ L ++GESG GKTTLGR I+ Sbjct: 309 LLQIKNLCTWYPIHNGLFGKTTDYVKAVDQLNFEVFPGETLGLVGESGCGKTTLGRTILR 368 Query: 61 LQKPTSGEVVYDGYNIWKNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWE 120 L +PTSGE++++G NI + +K RKD+Q+I QDPY++L ++ + ++ P L+ Sbjct: 369 LIQPTSGEIIFNGENITHIGKTALRKLRKDIQIIFQDPYASLNPKLSIGQSILEP-LQVH 427 Query: 121 KI--NKDELRKRLINLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVAD 178 K+ N E +++++ LL+ V L EE +YPH+ SGGQ+QR+ IAR+L++ P+ I+ D Sbjct: 428 KLYRNDSERKQKVLELLDKVGLK--EEHFNRYPHEFSGGQRQRVVIARALALQPKFIICD 485 Query: 179 EPVTMVDASLRIGILNTLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIV 238 E V+ +D S++ +LN + ++++ LT +FI+HD+ + + H+ D+ +VM G+I Sbjct: 486 ESVSALDVSVQAQVLNLIKDLQSEFGLTYIFISHDLAVVK---HISDR--ILVMNKGKIE 540 Query: 239 ERADLEEILKDPLHPYTNDLIKLTP 263 E E+I P YT LI+ P Sbjct: 541 EEGFPEQIFYAPKAAYTQKLIEAIP 565 Score = 139 bits (350), Expect = 2e-37 Identities = 81/263 (30%), Positives = 143/263 (54%), Gaps = 10/263 (3%) Query: 21 KKRKFYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTS----GEVVYDGYNI 76 +K F A+K +S + +G +L ++GESG+GK+ I+ L + GE+ ++ ++ Sbjct: 16 EKTWFKAVKQISFKVKKGTVLGIVGESGSGKSVTSFSIMRLHDERAAKITGEIDFEDISL 75 Query: 77 WKNKRKIFKKYR-KDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLL 135 ++ R + +I Q+P ++L T + I+ K+++ E +K I L Sbjct: 76 LNLSSNEIRQIRGNQISMIFQEPMTSLNPVFTCGYQVAEAIMLHRKVDQAEAKKHTIALF 135 Query: 136 ELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNT 195 V+L E+ YPHQ+SGGQKQR+ IA +LS +P++++ADEP T +D +++ IL Sbjct: 136 NEVQLPRPEKIFESYPHQISGGQKQRVMIAMALSCDPKLLIADEPTTALDVTVQKTILQL 195 Query: 196 LAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYT 255 L ++K N+ M+FI+HD+ + VM+ G IVE+ + I ++P HPYT Sbjct: 196 LLKLKQERNMAMIFISHDLGVVNEI-----ADEVAVMYKGEIVEQGPAKSIFENPQHPYT 250 Query: 256 NDLIKLTPSIDNLYKEINVKINY 278 L+ PS + K++ V ++ Sbjct: 251 KGLLACRPSPNRQLKKLPVVADF 273 Lambda K H 0.321 0.141 0.410 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 482 Number of extensions: 23 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 324 Length of database: 568 Length adjustment: 32 Effective length of query: 292 Effective length of database: 536 Effective search space: 156512 Effective search space used: 156512 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory